PRINCETON, Ore. — They implored the last holdout in the armed occupation of a wildlife refuge here to think about the Holy Spirit. They explained that the First Amendment was about freedom of speech and the Second was about the right to bear arms, and said that they were in that order for a reason. They asked him what he thought Jesus would have done in his situation.

He, in turn, asked for pizza and marijuana, criticized a government that condoned abortion and drone strikes, and talked about U.F.O.s and dying rather than going to prison.

In the final moments, a standoff fed by big ideas about the role of government came down Thursday morning to the grievances and fears of one troubled young man, and the tense but successful efforts of his sympathizers and F.B.I. agents to coax him to surrender, ending the occupation of Malheur National Wildlife Refuge in southeastern Oregon.

“I’m actually feeling suicidal right now,” said David Fry, 27, of Blanchester, Ohio, the last of the remaining protesters to leave the wildlife sanctuary, during telephone negotiations over his surrender. “I will not go another day as a slave to this system. I’m a free man. I will die a free man.”

In an extraordinary conclusion to the 40-day occupation, the four final holdouts, in a conversation streamed live online to tens of thousands of listeners, spoke with supporters trying to persuade them to give up, including Gavin Seim and KrisAnne Hall, both antigovernment activists; Michele Fiore, a Republican state legislator from Nevada; and the Rev. Franklin Graham, the evangelist. Three of the occupiers emerged in quick succession, hands raised in surrender, but Mr. Fry at first refused.

For the next hour and a quarter, sitting alone in a tent, hugging a blanket, he veered between resignation and agitation, rambling across a wide range of issues and conspiracy theories, as the audience listening on the live stream, operated by Mr. Seim, climbed as high as 30,000. Mr. Fry said that bankers caused wars, and that the government suppressed breakthrough inventions and was “chemically castrating everybody,” and occasionally he could be heard talking on another phone with the F.B.I.

Then, suddenly, it was over. “One more cookie, one more cigarette,” he said, just before leaving his hide-out. “Alrighty then.”

With the end of the standoff — which left one protester dead and 25 others indicted — the movement behind the occupation moved to a new phase. Ammon and Ryan Bundy, the brothers who spearheaded the occupation and now sit in a Portland jail, have vowed to escalate their fight, using the court as a platform.

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Thomas Wagner waved a flag near the Malheur National Wildlife Refuge on Thursday.CreditRebecca Boone/Associated Press

“Now we go from the refuge to our next battleground, which is the court system and legislation,” Ms. Fiore told reporters. She and Mr. Graham accompanied F.B.I. agents to the refuge Thursday, reassuring the holdouts as they gave themselves up, and she said she hugged each of them and the F.B.I. negotiators.

The occupation highlighted longstanding grievances over federal government ownership and management of vast acreage in the West. The Bundy brothers’ father, Cliven Bundy, a Nevada rancher, was arrested Wednesday on charges related to the armed standoff in 2014 between his supporters and federal agents. He and his supporters, like the Oregon occupiers, maintain that the federal government does not have the legal right to own so much land and is too restrictive on ranchers using it.

From the start, the Malheur standoff had a foot firmly planted in unfiltered live media, bypassing mainstream journalists, whom the protesters called tools of the government. Pete Santilli, who has an online talk show, was a frequent presence, interviewing and supporting the occupiers on his YouTube channel; he is among the jailed. Mr. Fry live streamed videos of the occupation and posted them online, while other protesters gave interviews on talk radio.

The occupiers repeatedly called on people from around the country to join them at the refuge. But the mass movement they hoped for never materialized. Critics said the protesters relied on a strained reading of the Constitution that the courts have rejected. And many experts argued that, in fact, ranchers — along with loggers, miners and others — get the use of federal land at bargain prices, heavily subsidized by taxpayers.

But Western lands experts and supporters of the occupation’s goals said that however quietly the standoff ended, and however garbled its message was at times, the deeper meaning will continue to resonate, because the occupiers in some ways reframed one of the nation’s oldest and thorniest arguments. The question of who should control land in the West — often a dry matter of economics in the past — has now been pulled into the polarized political terrain that has already made the nation a house divided.

In the 1980s and early ’90s, in what is now called the Sagebrush Rebellion, ranchers in the West protested higher prices that the federal government wanted to charge to let cattle graze on public lands. That fight, said David J. Hayes, a former deputy secretary of the Department of the Interior — the agency that oversees hundreds of millions of acres of Western lands — was largely over money.

The new argument, as the occupiers said repeatedly, is not overtly about money at all — rather, it is a much broader fight about the role of government and what constitutes federal overreach.

“The claim is that the land belongs to private parties, and that public ownership is a foreign concept in our Constitution,” said Mr. Hayes, who served in the Clinton and Obama administrations, and now teaches law at Stanford University. “That’s a relatively new one,” he added, “and it finds no credible support in the U.S. Constitution.”

However alien their arguments might seem to people in the East and in urban areas, where the federal government holds relatively little acreage, it has power in the rural West, where Washington controls more than half the land. But in this region, opinions were bitterly divided over the occupation; many people who supported its aims opposed its methods, and resented what they saw as interference and grandstanding by outsiders like the Bundys.

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A family waved a flag on Thursday in support of the last of the occupiers at Malheur Wildlife Refuge near Burns, Ore.CreditRob Kerr/Agence France-Presse — Getty Images

The occupation of the refuge, about six hours’ drive from Portland, began on Jan. 2. Armed militants demanded the release of two local ranchers who were imprisoned on arson charges for burning public lands. They also called for federal lands that had been in private hands, generations ago, to be turned over to ranchers or to local government.

The standoff appeared to be faltering in late January, when several prominent occupiers — including Ammon and Ryan Bundy — were arrested while venturing out of the refuge. A spokesman for the group, LaVoy Finicum, was killed, and several of the remaining occupiers heeded calls by the Bundys to go home.

But four of them held out for another two weeks, before revealing in a live-streamed conversation Wednesday that they intended to surrender on Thursday. They invoked the death of Mr. Finicum as evidence that the government did not want a peaceful conclusion, saying that they feared being killed, too.

On Thursday morning, Ms. Fiore urged the last four militants to surrender so they could continue to spread their message. “A dead man can’t talk, a dead man can’t write,” she told them. “We have to just stay together, stay alive.”

Sean Anderson, his wife, Sandy, and Jeff Banta emerged after 9:30 a.m. But Mr. Fry, still on the phone with Mr. Seim, Ms. Hall and an F.B.I. agent, resisted until almost 11 a.m.

“I’m paying taxes, and it’s going for abortion,” Mr. Fry said, and also for “murder of millions in the Middle East.” Later, he said, “My concern is that if I go to prison, I’ll probably be raped.”

In a telephone interview, Mr. Fry’s father, William Fry Jr., 56, said he had spoken with his son after the arrest. “He said, ‘Hi, I’m O.K., I’m going to be fine.’ ”

The two had been in contact during the occupation, and the elder Mr. Fry said he supported his son in “trying to make a change, to save our country from the problems that we’ve got.”

About 50 or 60 cars were parked at the roadblock outside the sanctuary on Thursday, where protest sympathizers mixed with journalists. Thomas Wagner, 32, an unemployed security guard from Christmas Valley, Ore., stood atop his pickup truck in full military fatigues, and said, “I came here to support these four patriots, to let them know that they are not being abandoned.”

In Burns, the town closest to the refuge, people raised American flags up and down the main street to celebrate the occupation’s end. “This is better than the Fourth of July,” said Bekka Riess, 15, beaming as she put flags up. “Maybe now we can finally get our town back.”